Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005749.1 Hibiscus syriacus cultivar Beakdansim tig00013446_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 235396
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1704 original size:14 final size:12
Alignment explanation
Indices: 1687--1729 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
1677 GCAAAAACAA
1687 AAAAGAAAAGAAGC
1 AAAA-AAAAGAA-C
1701 AAAAAAGAAGAAC
1 AAAAAA-AAGAAC
1714 -AAAAAAAGAAC
1 AAAAAAAAGAAC
1725 AAAAA
1 AAAAA
1730 TCAAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.22
12 9 0.33
13 3 0.11
14 9 0.33
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAC
Found at i:3486 original size:78 final size:78
Alignment explanation
Indices: 3318--3531 Score: 264
Period size: 78 Copynumber: 2.8 Consensus size: 78
3308 ATATCGTGCC
* * *
3318 ACTCGAGACAACACAAGTTCAACTTCACAACG-AAGAGA-CGACTGGTTGTCAAC--A-AA---C
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAAG-GACCG-CTCGTTGTCAACAAACAACTTC
3375 AACGAAGGATATTGG
64 AACGAAGGATATTGG
* * *
3390 ACTCCAGACAACACAAGTTCAACTTTATGACGAAAGGACCGCTGGTTGTCAACAAACAACTTCAA
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAAGGACCGCTCGTTGTCAACAAACAACTTCAA
3455 CGAAGGATATTGG
66 CGAAGGATATTGG
* * * *
3468 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTCGTTGTCAATAAACAATTTCA
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAAGGACCGCTCGTTGTCAACAAACAACTTCA
3532 TATTTCAGAG
Statistics
Matches: 123, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
72 42 0.34
73 5 0.04
74 1 0.01
75 2 0.02
78 73 0.59
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (78 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAAGGACCGCTCGTTGTCAACAAACAACTTCAA
CGAAGGATATTGG
Found at i:4529 original size:106 final size:106
Alignment explanation
Indices: 3452--4528 Score: 1671
Period size: 106 Copynumber: 10.2 Consensus size: 106
3442 CAAACAACTT
*
3452 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTCGTTGT
1 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
*
3517 CAATAAACAATTT--CATATTTCAGAGCCAATTTCAACTTCA
66 CAACAAACAATTTCCCA-ATTTCAGAGCCAATTTCAACTTCA
* * * *
3557 CAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACTGTTGGTTGT
1 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
* * *
3622 CAATAAACAACTTCCAAATTTCAGAGCCAATTTCAACTTCA
66 CAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
* *
3663 CAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGT
1 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
*
3728 CAACAAACAACTT--CAATTTCAGAGCCAATTTCAACTTCA
66 CAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
* *
3767 CAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGT
1 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
* *
3832 CAACAAACAACTTCCCAATTTCAGAGACAATTTCAACTTCA
66 CAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
* *
3873 CAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGT
1 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
* *
3938 CAACAAACAATTTCCCAATTTCGGAGCTAATTTCAACTTCA
66 CAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
* * *
3979 CAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGT
1 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
*
4044 CAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCA
66 CAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
* * * *
4085 CAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTTGTTGT
1 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
*
4150 CAACAAACAACTTT-TCAATTTCAGAGCCAATTTCAACTTCA
66 CAACAAACAA-TTTCCCAATTTCAGAGCCAATTTCAACTTCA
*
4191 CAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
1 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
*
4256 CAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
66 CAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
* * * *
4297 CAGCGAATGATATTGGACTCGAGACAACGCAAGTTCAACTTCAAGACGAAGGGACCGCTGGTTGT
1 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
* *
4362 CAACAAACAATTTCCCAATTTCGGAGCCAATTTTAACTTCA
66 CAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
* * * * *
4403 CAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGT
1 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
** *
4468 CAACAAACAATTTCCTGATTCCAGAGCCAATTTCAACTTCA
66 CAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
*
4509 CGAA-GGAGGATATTGGACTC
1 C-AACGAAGGATATTGGACTC
4529 GGAACAATGC
Statistics
Matches: 898, Mismatches: 67, Indels: 13
0.92 0.07 0.01
Matches are distributed among these distances:
104 99 0.11
105 74 0.08
106 719 0.80
107 6 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
CAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
Found at i:5294 original size:37 final size:37
Alignment explanation
Indices: 5209--5308 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 37
5199 TCGTCATACT
* * *
5209 AGGATTCAAACTCCTAAAAATAGGATAGAATTTTGCT
1 AGGATTCAAACTCCTAAAAATAGGATAGAATTCTACA
*
5246 AGGATTCAAACTCCTAAAAATAGGATAGAGTTCTACA
1 AGGATTCAAACTCCTAAAAATAGGATAGAATTCTACA
** * * *
5283 ATTATTTAAACTACTAAATATAGGAT
1 AGGATTCAAACTCCTAAAAATAGGAT
5309 CCACAAGCAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (37 bp):
AGGATTCAAACTCCTAAAAATAGGATAGAATTCTACA
Found at i:5852 original size:2 final size:2
Alignment explanation
Indices: 5845--5873 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5835 ATTTTCCTAT
5845 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5874 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5913 original size:17 final size:19
Alignment explanation
Indices: 5883--5921 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
5873 TTATTATTAT
5883 TTTATCTATGTTTACT-TA
1 TTTATCTATGTTTACTATA
*
5901 TTTA-CTATTTTTACTATA
1 TTTATCTATGTTTACTATA
5919 TTT
1 TTT
5922 TCCTAAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTATCTATGTTTACTATA
Found at i:6072 original size:2 final size:2
Alignment explanation
Indices: 6065--6096 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
6055 TACATACATT
6065 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6097 TTATTTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6265 original size:21 final size:21
Alignment explanation
Indices: 6239--6296 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
6229 TTTTATTCAA
*
6239 TTTCATTTTATTTATTTTTTG
1 TTTCATTTTATTTATTTTATG
** *
6260 TTTCA-TCCAATTATTTTATG
1 TTTCATTTTATTTATTTTATG
6280 TTT-ATTATTATTTATTT
1 TTTCATT-TTATTTATTT
6297 CATTTATTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
19 1 0.04
20 15 0.54
21 12 0.43
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.69
Consensus pattern (21 bp):
TTTCATTTTATTTATTTTATG
Found at i:16525 original size:27 final size:27
Alignment explanation
Indices: 16485--16549 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
16475 CATAATCTAA
*
16485 AACAAATTATTAATTATAATTATTAGATT
1 AACAAA-T-TTAATTATAATCATTAGATT
* * *
16514 AATAAATTTAATTATGATCATTATATT
1 AACAAATTTAATTATAATCATTAGATT
16541 AACAAATTT
1 AACAAATTT
16550 GATTTCTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 25 0.81
28 1 0.03
29 5 0.16
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (27 bp):
AACAAATTTAATTATAATCATTAGATT
Found at i:20145 original size:3 final size:3
Alignment explanation
Indices: 20137--20170 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
20127 AAGTAGGGGA
20137 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
20171 AGCTTAGGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:22516 original size:23 final size:24
Alignment explanation
Indices: 22471--22525 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
22461 TTATCAAATA
*
22471 ATTTAATTATATTCAATATTCAAT
1 ATTTAATTATATTCAATAATCAAT
*
22495 -TTTAATTATACTTTAA-AATCAAT
1 ATTTAATTATA-TTCAATAATCAAT
22518 ATTTAATT
1 ATTTAATT
22526 TTTCATTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTAATTATATTCAATAATCAAT
Found at i:22661 original size:15 final size:15
Alignment explanation
Indices: 22637--22668 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
22627 ATAAAGAAAC
22637 AATAAAAAAACAATA
1 AATAAAAAAACAATA
*
22652 AATAATAAAACAATA
1 AATAAAAAAACAATA
22667 AA
1 AA
22669 AACATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (15 bp):
AATAAAAAAACAATA
Found at i:28489 original size:120 final size:120
Alignment explanation
Indices: 28089--28542 Score: 601
Period size: 123 Copynumber: 3.7 Consensus size: 120
28079 GAATCAATCT
* * * * *
28089 AAGGTTGAACAAGTTATTCTTCA-GATGAACTTCTTCTTCCTTTTCAGATGAATTATTCTT-ATT
1 AAGGTTGAACAAGTTCTTC-TCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT-TTCATT
* * *
28152 ATGAAC-TCTTCCTGGCAATGCTAATGTTGATCTATCTCCCTT-TGTGATAGAATCAAGCGA
64 ACGAACTTCTT-CTGGAAATG-T--TGATGATCTATCT-CCTTCTGTGATAGAATCAAGCGA
* * * *
28212 AAGGTTGAACAAGTTCTTCTCATTATGAACTTATTTTTCCTCTTCAGATGAGTCCTTATCATTAC
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTTTCATTAC
28277 GAACTTCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCGA
66 GAACTTCTTCTGGAAATGTTGA---TGATCTATCTCCTTCTGTGATAGAATCAAGCGA
*
28335 AATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTTTCATTAC
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTTTCATTAC
* * *
28400 GAACTTCTTATGGAAATGTTGATGATCTATCTCCTTCTGTCATAGAATCAAGAGA
66 GAACTTCTTCTGGAAATGTTGATGATCTATCTCCTTCTGTGATAGAATCAAGCGA
* * * *
28455 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCATACGAGTTCTTCTCATTAC
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTTTCATTAC
*
28520 GAACTCCTTCTGGAAATGTTGAT
66 GAACTTCTTCTGGAAATGTTGAT
28543 CCATCGAGTG
Statistics
Matches: 297, Mismatches: 27, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
120 114 0.38
122 9 0.03
123 170 0.57
124 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (120 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTTTCATTAC
GAACTTCTTCTGGAAATGTTGATGATCTATCTCCTTCTGTGATAGAATCAAGCGA
Found at i:28523 original size:243 final size:245
Alignment explanation
Indices: 28092--28542 Score: 644
Period size: 243 Copynumber: 1.8 Consensus size: 245
28082 TCAATCTAAG
* *
28092 GTTGAACAAGTTATTCTTCAGATGAACTTCTTCTTCCTTTTCAGATGAATTATTCTTATTATGAA
1 GTTGAACAAGTTATTCTTCAGATGAACTTCTTCTTCCTCTTCAGATGAATTATTCTTATTACGAA
* * * * *
28157 CTCTTCCTGGCAATGCTAATGTTGATCTATCTCCCTTTGTGATAGAATCAAGCGAAAGGTTGAAC
66 CTCTTCATGGAAATGCT-ATGATGATCTATCTCCCTTTGTCATAGAATCAAGAGAAAGGTTGAAC
* * *
28222 AAGTTCTTCTCATTATGAACTTATTTTTCCTCTTCAGATGAGTCCTTATCATTACGAACTTCTTC
130 AAGTTCTTCTCATTATGAACTTATTCTTCCTCTTCAGACGAGTCCTTATCATTACGAACTCCTTC
28287 TGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCGAAAT
195 TGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCGAAAT
* * * *
28338 GTTGAACAAGTTCTTC-TCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT-TTCATTACG
1 GTTGAACAAGTTATTCTTCA-GATGAACTTCTTCTTCCTCTTCAGATGAATTATTCTT-ATTACG
28401 AACTTCTT-ATGGAAATG-T-TGATGATCTATCT-CCTTCTGTCATAGAATCAAGAGAAAGGTTG
64 AAC-TCTTCATGGAAATGCTATGATGATCTATCTCCCTT-TGTCATAGAATCAAGAGAAAGGTTG
* * * * *
28462 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCATACGAGTTCTTCTCATTACGAACTCC
127 AACAAGTTCTTCTCATTATGAACTTATTCTTCCTCTTCAGACGAGTCCTTATCATTACGAACTCC
28527 TTCTGGAAATGTTGAT
192 TTCTGGAAATGTTGAT
28543 CCATCGAGTG
Statistics
Matches: 182, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
242 4 0.02
243 108 0.59
245 6 0.03
246 60 0.33
247 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.40
Consensus pattern (245 bp):
GTTGAACAAGTTATTCTTCAGATGAACTTCTTCTTCCTCTTCAGATGAATTATTCTTATTACGAA
CTCTTCATGGAAATGCTATGATGATCTATCTCCCTTTGTCATAGAATCAAGAGAAAGGTTGAACA
AGTTCTTCTCATTATGAACTTATTCTTCCTCTTCAGACGAGTCCTTATCATTACGAACTCCTTCT
GGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCGAAAT
Found at i:29044 original size:21 final size:23
Alignment explanation
Indices: 29015--29060 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
29005 TTATAAAATA
*
29015 TTTATAAAAGAAT-AAATTGAAT
1 TTTATAAAAGAATAAAATGGAAT
29037 TTTA-AAAAGAATAAAATGGAAT
1 TTTATAAAAGAATAAAATGGAAT
29059 TT
1 TT
29061 GGGAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (23 bp):
TTTATAAAAGAATAAAATGGAAT
Found at i:44292 original size:14 final size:14
Alignment explanation
Indices: 44259--44356 Score: 67
Period size: 14 Copynumber: 6.8 Consensus size: 14
44249 TGCTTGAAAA
**
44259 AAAAAGAATGAATG
1 AAAAAGAAAAAATG
*
44273 AAAAAATGAAAAAGTG
1 -AAAAA-GAAAAAATG
44289 AAAAAGAAAAAATG
1 AAAAAGAAAAAATG
44303 AAAAAATGAAAAAAATG
1 -AAAAA-G-AAAAAATG
*
44320 AAAAA-AATGAAA--
1 AAAAAGAA-AAAATG
*
44332 AAAATGAAAAAATG
1 AAAAAGAAAAAATG
*
44346 AAAAGGAAAAA
1 AAAAAGAAAAA
44357 GAAAAATGAG
Statistics
Matches: 67, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.10
13 4 0.06
14 21 0.31
15 15 0.22
16 12 0.18
17 8 0.12
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAAAGAAAAAATG
Found at i:44293 original size:9 final size:8
Alignment explanation
Indices: 44269--44349 Score: 112
Period size: 8 Copynumber: 10.0 Consensus size: 8
44259 AAAAAGAATG
44269 AATGAAAA
1 AATGAAAA
44277 AATGAAAA
1 AATGAAAA
*
44285 AGTG-AAA
1 AATGAAAA
44292 AA-GAAAA
1 AATGAAAA
44299 AATGAAAA
1 AATGAAAA
44307 AATGAAAAA
1 AATG-AAAA
44316 AATGAAAAA
1 AATG-AAAA
44325 AATGAAAAA
1 AATG-AAAA
44334 AATGAAAA
1 AATGAAAA
44342 AATGAAAA
1 AATGAAAA
44350 GGAAAAAGAA
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
6 1 0.01
7 9 0.13
8 32 0.47
9 26 0.38
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (8 bp):
AATGAAAA
Found at i:44293 original size:17 final size:17
Alignment explanation
Indices: 44269--44349 Score: 116
Period size: 17 Copynumber: 4.9 Consensus size: 17
44259 AAAAAGAATG
44269 AATGAAAAAATG-AAAA
1 AATGAAAAAATGAAAAA
*
44285 AGTG-AAAAA-G-AAAA
1 AATGAAAAAATGAAAAA
44299 AATGAAAAAATGAAAAA
1 AATGAAAAAATGAAAAA
44316 AATGAAAAAAATGAAAAA
1 AATG-AAAAAATGAAAAA
44334 AATGAAAAAATGAAAA
1 AATGAAAAAATGAAAA
44350 GGAAAAAGAA
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.14
15 10 0.17
16 4 0.07
17 20 0.34
18 17 0.29
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (17 bp):
AATGAAAAAATGAAAAA
Found at i:45453 original size:105 final size:105
Alignment explanation
Indices: 45269--45960 Score: 1143
Period size: 105 Copynumber: 6.6 Consensus size: 105
45259 TCAACAACAA
* *
45269 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
45334 CCTAAAGGATAAGGTTCGTAATGAGAAGAGTATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
* *
45374 TCAAATCCACCGAAGAAGGAGGTGAACCAACATTTCTAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* * *
45439 CCGAAAGGAGAAGGTTCATAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
45479 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
45544 CCTAAAGGAGAAGGTTCGTAATGATAAGAGTATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
45584 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
45649 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCATT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
* *
45689 TCAAATCCACCGCAGAAGGAGGTGAA-CAATATTTCGAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* * *
45753 CATAAAGGAGAAGGTTCGTAATGAGAAGAGTATGTTTCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
45793 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAATAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
45858 CTTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
* * * *
45898 TCAAATTCACCCCAGAAGGAGGTGAATCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTC
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTC
45961 ATCCGGCAAA
Statistics
Matches: 547, Mismatches: 39, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
104 98 0.18
105 449 0.82
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (105 bp):
TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
Found at i:45745 original size:16 final size:16
Alignment explanation
Indices: 45724--45783 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
45714 ACAATATTTC
45724 GAGAAGAGTTCATAAT
1 GAGAAGAGTTCATAAT
* *
45740 GAGAAGAACTCGTCATAAAG
1 GAGAAG-AGT--TCAT-AAT
*
45760 GAGAAG-GTTCGTAAT
1 GAGAAGAGTTCATAAT
45775 GAGAAGAGT
1 GAGAAGAGT
45784 ATGTTTCTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
15 8 0.24
16 11 0.32
17 2 0.06
18 1 0.03
19 4 0.12
20 8 0.24
ACGTcount: A:0.42, C:0.08, G:0.30, T:0.20
Consensus pattern (16 bp):
GAGAAGAGTTCATAAT
Found at i:54555 original size:15 final size:15
Alignment explanation
Indices: 54535--54566 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
54525 TGTAATGAAT
54535 AATGAATGTATGCAA
1 AATGAATGTATGCAA
54550 AATGAATGTATGCAA
1 AATGAATGTATGCAA
54565 AA
1 AA
54567 GGTGTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:58258 original size:9 final size:9
Alignment explanation
Indices: 58230--58262 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
58220 ATATTATTCT
58230 TTAATTAAA
1 TTAATTAAA
*
58239 TT-ATAAAA
1 TTAATTAAA
58247 TTAATTAAA
1 TTAATTAAA
58256 TTAATTA
1 TTAATTA
58263 GCATAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTAATTAAA
Found at i:60968 original size:37 final size:37
Alignment explanation
Indices: 60918--60994 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
60908 CAACTCTGAT
60918 TAACCTTTCATCAAAGCCAACAACTTGATCTTTTGCA
1 TAACCTTTCATCAAAGCCAACAACTTGATCTTTTGCA
60955 TAACCTTTCATCAAAGCCAACAACTTGATCTTTTGCA
1 TAACCTTTCATCAAAGCCAACAACTTGATCTTTTGCA
60992 TAA
1 TAA
60995 ACTGATCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (37 bp):
TAACCTTTCATCAAAGCCAACAACTTGATCTTTTGCA
Found at i:61394 original size:15 final size:15
Alignment explanation
Indices: 61376--61470 Score: 115
Period size: 15 Copynumber: 6.5 Consensus size: 15
61366 TTCCGGAAAA
61376 TGAATTACTGGAATT
1 TGAATTACTGGAATT
61391 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
61406 TGAATTTCTGGAATT
1 TGAATTACTGGAATT
* **
61421 TGAATTTCTGGAAAA
1 TGAATTACTGGAATT
61436 TGAA--ACTGGAATT
1 TGAATTACTGGAATT
**
61449 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
61463 TGAATTAC
1 TGAATTAC
61471 ATTTCTGGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
13 10 0.14
14 12 0.17
15 47 0.68
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:61410 original size:30 final size:29
Alignment explanation
Indices: 61370--61470 Score: 143
Period size: 30 Copynumber: 3.5 Consensus size: 29
61360 TTGGTTTTCC
61370 GGAAAATGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGGAATTTGAATT-CT
** *
61400 GGAATTTGAATTTCTGGAATTTGAATTTCT
1 GGAAAATGAATTACTGGAATTTGAA-TTCT
61430 GGAAAATGAA--ACTGGAATTTGAATTCT
1 GGAAAATGAATTACTGGAATTTGAATTCT
61457 GGAAAATGAATTAC
1 GGAAAATGAATTAC
61471 ATTTCTGGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
27 14 0.23
28 12 0.19
29 2 0.03
30 32 0.52
31 2 0.03
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.35
Consensus pattern (29 bp):
GGAAAATGAATTACTGGAATTTGAATTCT
Found at i:61476 original size:20 final size:20
Alignment explanation
Indices: 61453--61502 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
61443 GGAATTTGAA
61453 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
61473 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
61493 TTCTGGAAAA
1 TTCTGGAAAA
61503 CGTTTTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:61901 original size:30 final size:28
Alignment explanation
Indices: 61844--62000 Score: 89
Period size: 30 Copynumber: 5.5 Consensus size: 28
61834 TAATATTATC
**
61844 ATTATT-AAATATATAAAAAATTATTATAT
1 ATTATTAAAATA-ATAAATTATT-TTATAT
61873 ATTATTAAAATAA-AAATATATATCTTATATT
1 ATTATTAAAATAATAAAT-TAT-T-TTATA-T
* *
61904 ATTA-TAATATAATTAATTATTTTATAT
1 ATTATTAAAATAATAAATTATTTTATAT
* *
61931 AATATTAAAAT-AT-AA-TATTATAT-T
1 ATTATTAAAATAATAAATTATTTTATAT
*
61955 ATTA-TAAATATTAATAAATATATTTTAAAT
1 ATTATTAAA-A-TAATAAAT-TATTTTATAT
61985 ATT-TTAATAATTAATA
1 ATTATTAA-AA-TAATA
62001 TTTTGATGAA
Statistics
Matches: 102, Mismatches: 11, Indels: 29
0.72 0.08 0.20
Matches are distributed among these distances:
23 4 0.04
24 5 0.05
25 8 0.08
26 4 0.04
27 8 0.08
28 13 0.13
29 16 0.16
30 35 0.34
31 9 0.09
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTATTAAAATAATAAATTATTTTATAT
Found at i:61915 original size:56 final size:54
Alignment explanation
Indices: 61815--61979 Score: 135
Period size: 56 Copynumber: 3.0 Consensus size: 54
61805 CTTTACTAAA
* * *
61815 ATATTATGAAATATATAAATA-ATA-TTATCATTATTAAATATATAAAAAATTATTAT
1 ATATTATTAAA-ATAAAAATATATATTTAT-ATTATTATA-ATATAAAAAATTATT-T
**
61871 ATATTATTAAAATAAAAATATATATCTTATATTATTATAATATAATTAATTATTT
1 ATATTATTAAAATAAAAATATATAT-TTATATTATTATAATATAAAAAATTATTT
* * *
61926 -TA-TA-TAATATTAAAATATA-ATATTATATTATTATAAATATTAATAAATATATTT
1 ATATTATTAAAATAAAAATATATAT-TTATATTATTAT-AATA-TAAAAAAT-TATTT
61980 TAAATATTTT
Statistics
Matches: 94, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
51 14 0.15
52 17 0.18
53 9 0.10
54 7 0.07
55 9 0.10
56 26 0.28
57 8 0.09
58 4 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (54 bp):
ATATTATTAAAATAAAAATATATATTTATATTATTATAATATAAAAAATTATTT
Found at i:61957 original size:21 final size:23
Alignment explanation
Indices: 61927--61994 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
61917 TAATTATTTT
*
61927 ATATAATATTAAAATA-TAAT-A
1 ATATATTATTAAAATATTAATAA
*
61948 TTATATTATTATAAATATTAATAA
1 ATATATTATTA-AAATATTAATAA
*
61972 ATATATT-TTAAATATTTTAATAA
1 ATATATTATTAAA-ATATTAATAA
61995 TTAATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 9 0.23
22 7 0.18
23 16 0.41
24 7 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATATTATTAAAATATTAATAA
Found at i:61962 original size:23 final size:24
Alignment explanation
Indices: 61897--61970 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 24
61887 AATATATATC
*
61897 TTATATTATTATAATATAATTAATTA
1 TTATATTATTATAAAAT-ATTAA-TA
* *
61923 TTTTATATAATATTAAAATA-TAATA
1 TTATAT-TATTA-TAAAATATTAATA
61948 TTATATTATTAT-AAATATTAATA
1 TTATATTATTATAAAATATTAATA
61971 AATATATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 5 0.12
23 6 0.15
24 4 0.10
25 7 0.17
26 8 0.20
27 5 0.12
28 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTATATTATTATAAAATATTAATA
Found at i:62293 original size:42 final size:42
Alignment explanation
Indices: 62176--62295 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
62166 ATGAATTACA
* *
62176 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
62218 TTCCGGAAAACAAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
62260 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
62296 TTCAGGGAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:70782 original size:17 final size:18
Alignment explanation
Indices: 70760--70793 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
70750 TTTGGTGCAG
*
70760 AGGGAATCGA-TCCCCCC
1 AGGGAACCGATTCCCCCC
70777 AGGGAACCGATTCCCCC
1 AGGGAACCGATTCCCCC
70794 TTTGAAGGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.41, G:0.24, T:0.12
Consensus pattern (18 bp):
AGGGAACCGATTCCCCCC
Found at i:70825 original size:21 final size:21
Alignment explanation
Indices: 70799--70838 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
70789 CCCCCTTTGA
*
70799 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
70820 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
70839 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:70921 original size:20 final size:21
Alignment explanation
Indices: 70898--70980 Score: 69
Period size: 22 Copynumber: 3.9 Consensus size: 21
70888 TTGGTGCAGA
*
70898 GGGAATCGATCCCCCCCTGA-
1 GGGAACCGATCCCCCCCTGAG
* **
70918 GGGAACCGATTCCCCTTTGAAG
1 GGGAACCGATCCCCCCCTG-AG
**
70940 GGGAACCGATTCCCCCCCACAG
1 GGGAACCGA-TCCCCCCCTGAG
* *
70962 GGGAATCGATACCCCCCTG
1 GGGAACCGATCCCCCCCTG
70981 GGGTTCTGTT
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
20 15 0.32
21 8 0.17
22 19 0.40
23 5 0.11
ACGTcount: A:0.22, C:0.37, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAACCGATCCCCCCCTGAG
Found at i:70991 original size:140 final size:139
Alignment explanation
Indices: 70742--71020 Score: 501
Period size: 140 Copynumber: 2.0 Consensus size: 139
70732 AAAGTCGGAT
70742 TTTAGCATTTTGGTGCAGAGGGAATCGATCCCCCCAGGGAACCGATTCCCCCTTTGAAGGGGAAC
1 TTTAGCATTTTGGTGCAGAGGGAATCGATCCCCCCAGGGAACCGATTCCCCCTTTGAAGGGGAAC
70807 CGATTCCCCCCACAGGGGAATCGATACCCCCCTGGGGTTCTGTTAAATCGGGCAG-ACACCCC-A
66 CGATTCCCCCCACAGGGGAATCGATACCCCCCTGGGGTTCTGTTAAATCGGGCAGAACACCCCAA
70870 AAAACCCAA
131 AAAACCCAA
70879 TTTAGCATTTTGGTGCAGAGGGAATCGATCCCCCCCTGAGGGAACCGATT-CCCCTTTGAAGGGG
1 TTTAGCATTTTGGTGCAGAGGGAATCGAT-CCCCCC--AGGGAACCGATTCCCCCTTTGAAGGGG
70943 AACCGATTCCCCCCCACAGGGGAATCGATACCCCCCTGGGGTTCTGTTAAATCGGGCAGAACACC
63 AACCGATT-CCCCCCACAGGGGAATCGATACCCCCCTGGGGTTCTGTTAAATCGGGCAGAACACC
71008 CCAAAAAACCCAA
127 CCAAAAAACCCAA
71021 AAACCCTTCT
Statistics
Matches: 136, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
137 29 0.21
138 6 0.04
139 22 0.16
140 62 0.46
141 7 0.05
142 10 0.07
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.19
Consensus pattern (139 bp):
TTTAGCATTTTGGTGCAGAGGGAATCGATCCCCCCAGGGAACCGATTCCCCCTTTGAAGGGGAAC
CGATTCCCCCCACAGGGGAATCGATACCCCCCTGGGGTTCTGTTAAATCGGGCAGAACACCCCAA
AAAACCCAA
Found at i:72940 original size:17 final size:17
Alignment explanation
Indices: 72915--72948 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
72905 TTGAATATTT
*
72915 TGGAATGTTTGATTTTG
1 TGGAATGTTGGATTTTG
*
72932 TGGATTGTTGGATTTTG
1 TGGAATGTTGGATTTTG
72949 GATTTATGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.32, T:0.53
Consensus pattern (17 bp):
TGGAATGTTGGATTTTG
Found at i:82337 original size:31 final size:31
Alignment explanation
Indices: 82281--82381 Score: 116
Period size: 31 Copynumber: 3.3 Consensus size: 31
82271 TTTTTGATCC
* *
82281 TTAAACTT-TCAAA-TATTACATAATAATCA
1 TTAAATTTATCAAATTATTACAAAATAATCA
* * *
82310 TTTAATTTATCGAATTATTATAAAATAATCA
1 TTAAATTTATCAAATTATTACAAAATAATCA
* * *
82341 TTAAACTTATCAAATTATTACAAAATAGTTA
1 TTAAATTTATCAAATTATTACAAAATAATCA
82372 TTAAATTTAT
1 TTAAATTTAT
82382 TACTATTTAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
29 6 0.10
30 4 0.07
31 48 0.83
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (31 bp):
TTAAATTTATCAAATTATTACAAAATAATCA
Found at i:83567 original size:2 final size:2
Alignment explanation
Indices: 83560--83591 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
83550 CCCTGTATGA
83560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
83592 GTATGTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84983 original size:336 final size:343
Alignment explanation
Indices: 84339--85018 Score: 1311
Period size: 336 Copynumber: 2.0 Consensus size: 343
84329 CTCTGAGGTG
84339 TGTTTGGTTGGCATTCTCGAATGAAATTTATATTCATCTGTTTGGTTGATTGGGAATGTCATTCC
1 TGTTTGGTTGGCATTCTCGAATGAAATTTATATTCATCTGTTTGGTTGATTGGGAATGTCATTCC
84404 CGGTAATCTTACATTATCAATAGTAAATTTTTTGAGGTATATTACCGGGAATGTCATTGCCTCCA
66 CGGTAATCTTACATTATCAATAGTAAATTTTTTGAGGTATATTACCGGGAATGTCATTGCCTCCA
84469 TTTACTTAAGTATTGTTGGATTACCGACGTTTTGGACTAAAATGCCCTTAATTTTTTTTTTCTTT
131 TTTACTTAAGTATTGTTGGATTACCGACGTTTTGGACTAAAATGCCCTTAATTTTTTTTTTCTTT
84534 CAAAAATATTATTATTCTATCATTGAATAATAAAAATTCTACGAAAGTTAAATTATAAATTTATC
196 CAAAAATATTATTATTCTATCATTGAATAATAAAAATTCTACGAAAGTTAAATTATAAATTTATC
84599 TTTAAACTATTTTAGATTTATGAAAAAAGTCTATAATTAAACTTTTATATGAAATTCA-GGGTTA
261 TTTAAACTATTTTAGATTTATGAAAAAAGTCTATAATTAAACTTTTATATGAAATTCAGGGGTTA
84663 AAAT-AAATTTTACCCTT
326 AAATAAAATTTTACCCTT
84680 TGTTTGGTTGGCATTCTCGAATGAAA-TTATATTCATCTGTTTGGTTGATTGGGAATGTCATTCC
1 TGTTTGGTTGGCATTCTCGAATGAAATTTATATTCATCTGTTTGGTTGATTGGGAATGTCATTCC
84744 CGGTAATCTTACATTATCAATAGTAAA-TTTTTGAGG-ATATTACC-GGAATGTCATTGCCTCCA
66 CGGTAATCTTACATTATCAATAGTAAATTTTTTGAGGTATATTACCGGGAATGTCATTGCCTCCA
84806 TTTACTTAAGTA-TGTTGGATTACCGACGTTTTGGACTAAAATGCCCTTAATTTTTTTTTTCTTT
131 TTTACTTAAGTATTGTTGGATTACCGACGTTTTGGACTAAAATGCCCTTAATTTTTTTTTTCTTT
84870 CAAAAATATTATTATTCTATCATTGAATAATAAAAATTCTACGAAAGTTAAATTATAAATTTATC
196 CAAAAATATTATTATTCTATCATTGAATAATAAAAATTCTACGAAAGTTAAATTATAAATTTATC
84935 TTTAAACTATTTTAGATTTATGAAAAAAGTCTATAATTAAACTTTTATATGAAATTCAGGGGTTA
261 TTTAAACTATTTTAGATTTATGAAAAAAGTCTATAATTAAACTTTTATATGAAATTCAGGGGTTA
85000 AAATAAAATTTTACCCTT
326 AAATAAAATTTTACCCTT
85018 T
1 T
85019 CATTAAATCT
Statistics
Matches: 337, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
336 175 0.52
337 40 0.12
338 22 0.07
339 9 0.03
340 65 0.19
341 26 0.08
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (343 bp):
TGTTTGGTTGGCATTCTCGAATGAAATTTATATTCATCTGTTTGGTTGATTGGGAATGTCATTCC
CGGTAATCTTACATTATCAATAGTAAATTTTTTGAGGTATATTACCGGGAATGTCATTGCCTCCA
TTTACTTAAGTATTGTTGGATTACCGACGTTTTGGACTAAAATGCCCTTAATTTTTTTTTTCTTT
CAAAAATATTATTATTCTATCATTGAATAATAAAAATTCTACGAAAGTTAAATTATAAATTTATC
TTTAAACTATTTTAGATTTATGAAAAAAGTCTATAATTAAACTTTTATATGAAATTCAGGGGTTA
AAATAAAATTTTACCCTT
Found at i:87809 original size:83 final size:83
Alignment explanation
Indices: 87722--87880 Score: 257
Period size: 83 Copynumber: 1.9 Consensus size: 83
87712 ATATCTATTT
* * *
87722 AATATTTTAAATTTAAAATATATTATTATCTGTTTAAATTTAGATATTAAAAGATATCTT-GGTG
1 AATATTTTAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAAGAGAT-TTAGGTG
87786 GAGTAAAACTCTTAGGTTC
65 GAGTAAAACTCTTAGGTTC
*
87805 AATATTTTAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAAGAGATTTAGTTGG
1 AATATTTTAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAAGAGATTTAGGTGG
*
87870 AGTAAAGCTCT
66 AGTAAAACTCT
87881 CTCGAAATTC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
82 2 0.03
83 68 0.97
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (83 bp):
AATATTTTAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAAGAGATTTAGGTGG
AGTAAAACTCTTAGGTTC
Found at i:89122 original size:19 final size:20
Alignment explanation
Indices: 89070--89120 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
89060 GTTAAGGGAT
*
89070 GTATTGATACCCTATAGGGG
1 GTATCGATACCCTATAGGGG
89090 GTATCGATACCCTATAGGGG
1 GTATCGATACCCTATAGGGG
89110 GTATCGATACC
1 GTATCGATACC
89121 TACTTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (20 bp):
GTATCGATACCCTATAGGGG
Found at i:91548 original size:20 final size:20
Alignment explanation
Indices: 91525--91568 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
91515 TAAATAGTCA
91525 CGATGCTATTTAAACAGTAC
1 CGATGCTATTTAAACAGTAC
* * *
91545 CGATGTTGTTTAAACAGTAT
1 CGATGCTATTTAAACAGTAC
91565 CGAT
1 CGAT
91569 ACTGTTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
CGATGCTATTTAAACAGTAC
Found at i:91574 original size:20 final size:20
Alignment explanation
Indices: 91533--91575 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
91523 CACGATGCTA
**
91533 TTTAAACAGTACCGATGTTG
1 TTTAAACAGTACCGATACTG
*
91553 TTTAAACAGTATCGATACTG
1 TTTAAACAGTACCGATACTG
91573 TTT
1 TTT
91576 GAATAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (20 bp):
TTTAAACAGTACCGATACTG
Found at i:91785 original size:20 final size:22
Alignment explanation
Indices: 91747--91786 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
91737 TTTGAGTAGA
91747 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
91769 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
91787 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:95626 original size:13 final size:13
Alignment explanation
Indices: 95608--95638 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
95598 TTAAAATATA
95608 AAAATGATGTTTC
1 AAAATGATGTTTC
95621 AAAATGATGTTTC
1 AAAATGATGTTTC
95634 AAAAT
1 AAAAT
95639 TGAAAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (13 bp):
AAAATGATGTTTC
Found at i:101426 original size:14 final size:14
Alignment explanation
Indices: 101407--101438 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
101397 CGTTCGTGAA
101407 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
101421 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
101435 CGTT
1 CGTT
101439 TATGTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:101455 original size:24 final size:24
Alignment explanation
Indices: 101408--101458 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
101398 GTTCGTGAAC
* *
101408 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
* *
101432 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
101456 GTT
1 GTT
101459 TAACCCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCAGTTAT
Found at i:102349 original size:23 final size:23
Alignment explanation
Indices: 102316--102360 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
102306 TGTTGACCTT
* *
102316 GAATCATGCTTGAATCGAGCTCA
1 GAATCAAGCTTCAATCGAGCTCA
102339 GAATCAAGCTTCAATCGAGCTC
1 GAATCAAGCTTCAATCGAGCTC
102361 GAGTCTCGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (23 bp):
GAATCAAGCTTCAATCGAGCTCA
Found at i:102755 original size:16 final size:16
Alignment explanation
Indices: 102734--102766 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
102724 AAAAAAAAAT
102734 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
102750 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
102766 T
1 T
102767 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:103523 original size:21 final size:20
Alignment explanation
Indices: 103499--103537 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
103489 TTAACCATTA
*
103499 TGTTAAGAAAGAAATATTTGT
1 TGTTAACAAA-AAATATTTGT
*
103520 TGTTGACAAAAAATATTT
1 TGTTAACAAAAAATATTT
103538 CTTTTAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTTAACAAAAAATATTTGT
Found at i:103970 original size:19 final size:19
Alignment explanation
Indices: 103946--103995 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
103936 TGTAATATGG
103946 GTACCGATACACAGCTAAT
1 GTACCGATACACAGCTAAT
103965 GTACCGATACACAGCTAAT
1 GTACCGATACACAGCTAAT
103984 GTACCGATACAC
1 GTACCGATACAC
103996 TCTAGGCTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (19 bp):
GTACCGATACACAGCTAAT
Found at i:109496 original size:20 final size:20
Alignment explanation
Indices: 109471--109508 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
109461 TTTTGGTGCA
*
109471 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
109491 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
109509 TTTGAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:110749 original size:25 final size:25
Alignment explanation
Indices: 110721--110784 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
110711 AACAAAAAGG
110721 GGGAGAAGTGTTAAGTGTTTTAAAT
1 GGGAGAAGTGTTAAGTGTTTTAAAT
110746 GGGAGAAGTGTTAAGTGTTTTAAAT
1 GGGAGAAGTGTTAAGTGTTTTAAAT
110771 GGGAGAAGTGTTAA
1 GGGAGAAGTGTTAA
110785 AGTAAGGGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.34, T:0.33
Consensus pattern (25 bp):
GGGAGAAGTGTTAAGTGTTTTAAAT
Found at i:113022 original size:21 final size:19
Alignment explanation
Indices: 112981--113038 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 19
112971 CAACAATTGA
112981 TAACAATTGGTAT-TTTTT
1 TAACAATTGGTATCTTTTT
*
112999 TAACAATTGATATTCTTTTGT
1 TAACAATTGGTA-TCTTTT-T
113020 TAACAATTGGTATCTTTTT
1 TAACAATTGGTATCTTTTT
113039 CATTAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 11 0.31
19 2 0.06
20 10 0.29
21 12 0.34
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.53
Consensus pattern (19 bp):
TAACAATTGGTATCTTTTT
Found at i:114499 original size:31 final size:30
Alignment explanation
Indices: 114461--114577 Score: 99
Period size: 31 Copynumber: 3.8 Consensus size: 30
114451 GAGTTGAGGG
* *
114461 TTACCTATGTACTTCGGGATATATGGACAGT
1 TTACCTATGT-CTTCGAGACATATGGACAGT
* * * *
114492 TTACCTATGTCCTTTGAGACGTATGAACAAT
1 TTACCTATGT-CTTCGAGACATATGGACAGT
* * *
114523 TTATCTATGTCTTTCCAGACATATGGACAGG
1 TTACCTATGTC-TTCGAGACATATGGACAGT
* *
114554 TTACCTATGTTCTACGAAACATAT
1 TTACCTATG-TCTTCGAGACATAT
114578 AGATGGTGGT
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
30 1 0.02
31 63 0.95
32 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (30 bp):
TTACCTATGTCTTCGAGACATATGGACAGT
Found at i:115487 original size:29 final size:29
Alignment explanation
Indices: 115445--115533 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
115435 GGGTTGGGGT
115445 GTTACAATGTCCTTTGGGACATATGGATA
1 GTTACAATGTCCTTTGGGACATATGGATA
*
115474 GTTACAATGTCCTTTGGGACATATGGACA
1 GTTACAATGTCCTTTGGGACATATGGATA
* * * * *
115503 ATTACCTATGTTCTTCGGAACATATGGATA
1 GTTA-CAATGTCCTTTGGGACATATGGATA
115533 G
1 G
115534 GTCCTTCGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 31 0.61
30 20 0.39
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (29 bp):
GTTACAATGTCCTTTGGGACATATGGATA
Found at i:119415 original size:117 final size:117
Alignment explanation
Indices: 119209--119442 Score: 459
Period size: 117 Copynumber: 2.0 Consensus size: 117
119199 CGGGTTAATG
119209 AACATTGCTCTTATTGAATAATCAAACCTAGAAAGCTCTAGACTTGATGAAGAACAATGGGGAAT
1 AACATTGCTCTTATTGAATAATCAAACCTAGAAAGCTCTAGACTTGATGAAGAACAATGGGGAAT
119274 GAATAGGGGAAGGTGGCGGCAGCAAGTAGGGTTCTTAAAGTTTTTTTTAGGT
66 GAATAGGGGAAGGTGGCGGCAGCAAGTAGGGTTCTTAAAGTTTTTTTTAGGT
*
119326 AACATTGCTCTTGTTGAATAATCAAACCTAGAAAGCTCTAGACTTGATGAAGAACAATGGGGAAT
1 AACATTGCTCTTATTGAATAATCAAACCTAGAAAGCTCTAGACTTGATGAAGAACAATGGGGAAT
119391 GAATAGGGGAAGGTGGCGGCAGCAAGTAGGGTTCTTAAAGTTTTTTTTAGGT
66 GAATAGGGGAAGGTGGCGGCAGCAAGTAGGGTTCTTAAAGTTTTTTTTAGGT
119443 TCTGGAAACA
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 116 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (117 bp):
AACATTGCTCTTATTGAATAATCAAACCTAGAAAGCTCTAGACTTGATGAAGAACAATGGGGAAT
GAATAGGGGAAGGTGGCGGCAGCAAGTAGGGTTCTTAAAGTTTTTTTTAGGT
Found at i:123736 original size:7 final size:8
Alignment explanation
Indices: 123707--123747 Score: 55
Period size: 8 Copynumber: 4.8 Consensus size: 8
123697 AAAATTTAGC
123707 TTTTTTGTT
1 TTTTTTG-T
123716 TTTTTTGCCT
1 TTTTTTG--T
123726 TTTTTTGT
1 TTTTTTGT
123734 TTTTTTGT
1 TTTTTTGT
123742 TTTTTT
1 TTTTTT
123748 TAAATAGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 15 0.50
9 7 0.23
10 8 0.27
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (8 bp):
TTTTTTGT
Found at i:124522 original size:11 final size:11
Alignment explanation
Indices: 124503--124532 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
124493 GGTCCTAAAT
124503 AATTAAATAATA
1 AATT-AATAATA
124515 AATTAATAATA
1 AATTAATAATA
124526 AATTAAT
1 AATTAAT
124533 CATGTCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTAATAATA
Found at i:127078 original size:22 final size:22
Alignment explanation
Indices: 127044--127085 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
127034 ATAATTATTT
127044 AAAAAATTAAATA-AAAATATC
1 AAAAAATTAAATAGAAAATATC
*
127065 AAAAATATTTAATAGAAAATA
1 AAAAA-ATTAAATAGAAAATA
127086 ATTTTGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAAATTAAATAGAAAATATC
Found at i:127501 original size:16 final size:16
Alignment explanation
Indices: 127476--127506 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
127466 TTCTAAATTT
*
127476 TTTTTTGAGTTCAAGC
1 TTTTTCGAGTTCAAGC
127492 TTTTTCGAGTTCAAG
1 TTTTTCGAGTTCAAG
127507 TTTCAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCAAGC
Found at i:128345 original size:17 final size:17
Alignment explanation
Indices: 128323--128365 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
128313 AAAATTGAAA
128323 TTTAATTTACATTAAAT
1 TTTAATTTACATTAAAT
128340 TTTAATTTACATTAAAT
1 TTTAATTTACATTAAAT
128357 TTTAATTTA
1 TTTAATTTA
128366 TGTTATTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAATTTACATTAAAT
Found at i:128724 original size:21 final size:21
Alignment explanation
Indices: 128700--128741 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
128690 CATTTTTAAT
128700 TTATAGAATTACAATTAAATA
1 TTATAGAATTACAATTAAATA
128721 TTATAGAATTACAATTAAATA
1 TTATAGAATTACAATTAAATA
128742 ATATTTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
TTATAGAATTACAATTAAATA
Found at i:128794 original size:29 final size:28
Alignment explanation
Indices: 128749--128803 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
128739 ATAATATTTG
*
128749 TAAAATTGTATTAATTTTAGACTTAATA
1 TAAAATTATATTAATTTTAGACTTAATA
* *
128777 TAAAATATATATTCATTTTATACTTAA
1 TAAAAT-TATATTAATTTTAGACTTAA
128804 ATTTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (28 bp):
TAAAATTATATTAATTTTAGACTTAATA
Found at i:133201 original size:35 final size:34
Alignment explanation
Indices: 133117--133203 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
133107 AAAAAAAAAT
*
133117 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
133151 TAAATAGTAAAAAAATTACAATAACTGATATTAAATGG
1 TAAATA-CAACAAAATTACAATAA--G-TATTAAATGG
133189 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
133204 ACAAAATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 6 0.13
35 23 0.51
37 5 0.11
38 11 0.24
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:133216 original size:13 final size:13
Alignment explanation
Indices: 133198--133222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
133188 GTAATAAACA
133198 AAATTAACAAAAT
1 AAATTAACAAAAT
133211 AAATTAACAAAA
1 AAATTAACAAAA
133223 AGTCCAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATTAACAAAAT
Found at i:133234 original size:34 final size:34
Alignment explanation
Indices: 133194--133287 Score: 125
Period size: 36 Copynumber: 2.7 Consensus size: 34
133184 AATGGTAATA
*
133194 AACAAAATTAACAAAATAAATTAACAAAAAGTCC
1 AACAAAATTAACAAAATAAATTAAAAAAAAGTCC
***
133228 AACAAAATTAACAAAATTTTTTTTAAAAAAAAGTCC
1 AACAAAATTAACAAAA--TAAATTAAAAAAAAGTCC
*
133264 AACCAAATTAACAAAATAAATTAA
1 AACAAAATTAACAAAATAAATTAA
133288 GTATTAAATG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
34 21 0.42
36 29 0.58
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.23
Consensus pattern (34 bp):
AACAAAATTAACAAAATAAATTAAAAAAAAGTCC
Found at i:133320 original size:14 final size:14
Alignment explanation
Indices: 133301--133334 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
133291 TTAAATGATA
133301 AATAAAAAAATTAC
1 AATAAAAAAATTAC
*
133315 AATAAAAAAATTCC
1 AATAAAAAAATTAC
133329 AATAAA
1 AATAAA
133335 CAAGTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAAAAAAATTAC
Found at i:135103 original size:32 final size:30
Alignment explanation
Indices: 135067--135125 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
135057 GGGGCCACGG
*
135067 GGCCTATCTAAGAATACATCTTAGGGCCGCAA
1 GGCCTA-CCAAGAAT-CATCTTAGGGCCGCAA
* *
135099 GGCCTACCGAGAATGATCTTAGGGCCG
1 GGCCTACCAAGAATCATCTTAGGGCCG
135126 TAGAGCCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.50
31 6 0.25
32 6 0.25
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.20
Consensus pattern (30 bp):
GGCCTACCAAGAATCATCTTAGGGCCGCAA
Found at i:144421 original size:16 final size:16
Alignment explanation
Indices: 144397--144466 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
144387 ATAACTGCAA
* *
144397 AAAAAATTAATTAAAT
1 AAAATATTAAATAAAT
*
144413 AAAATATTAAAAAAAT
1 AAAATATTAAATAAAT
144429 -AAATAGTT-AA-AAAT
1 AAAATA-TTAAATAAAT
144443 AACAAATATTAAATAAA-
1 -A-AAATATTAAATAAAT
144460 AAAATAT
1 AAAATAT
144467 ACTTAAAGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.09
15 13 0.29
16 18 0.40
17 7 0.16
18 3 0.07
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:144432 original size:15 final size:15
Alignment explanation
Indices: 144409--144466 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
144399 AAAATTAATT
144409 AAATAAAATATTAAAA
1 AAAT-AAATATTAAAA
144425 AAATAAATAGTTAAAA
1 AAATAAATA-TTAAAA
*
144441 ATAACAAATATTAAATA
1 A-AATAAATATTAAA-A
144458 AAA-AAATAT
1 AAATAAATAT
144467 ACTTAAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
15 11 0.29
16 18 0.47
17 9 0.24
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (15 bp):
AAATAAATATTAAAA
Found at i:157777 original size:70 final size:70
Alignment explanation
Indices: 157662--157799 Score: 249
Period size: 70 Copynumber: 2.0 Consensus size: 70
157652 TTCTGAATTC
*
157662 ACTTTGATGATGTAGGGTCCTTGTGCTTAAGATCTATGTTGCTCGGACTCTACATTTTTCACTAA
1 ACTTTGATGATGTAAGGTCCTTGTGCTTAAGATCTATGTTGCTCGGACTCTACATTTTTCACTAA
157727 GTACT
66 GTACT
* *
157732 ACTTTGATGATGTAAGGTCCTTGTGCTTAAGATCTATGTTTCTCGGACTCTACATTTTTCTCTAA
1 ACTTTGATGATGTAAGGTCCTTGTGCTTAAGATCTATGTTGCTCGGACTCTACATTTTTCACTAA
157797 GTA
66 GTA
157800 GCCGTGTCTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (70 bp):
ACTTTGATGATGTAAGGTCCTTGTGCTTAAGATCTATGTTGCTCGGACTCTACATTTTTCACTAA
GTACT
Found at i:160125 original size:28 final size:28
Alignment explanation
Indices: 160088--160143 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
160078 GTTTTACTTG
*
160088 TTTGCATTAATGAGTACTGAAAATGTAC
1 TTTGCATTAATGAGCACTGAAAATGTAC
*
160116 TTTGCATTAATGAGCATTGAAAATGTAC
1 TTTGCATTAATGAGCACTGAAAATGTAC
160144 AGTTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (28 bp):
TTTGCATTAATGAGCACTGAAAATGTAC
Found at i:165592 original size:14 final size:14
Alignment explanation
Indices: 165573--165605 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
165563 AAAATATATC
165573 ATTTTATTTT-ATTT
1 ATTTTATTTTGA-TT
165587 ATTTTATTTTGATT
1 ATTTTATTTTGATT
165601 ATTTT
1 ATTTT
165606 TAAGTATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (14 bp):
ATTTTATTTTGATT
Found at i:165708 original size:23 final size:21
Alignment explanation
Indices: 165676--165729 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
165666 ATTGTTTAGG
*
165676 ATTAATTTTTAAAATGTTTTCAT
1 ATTAA-TTTTAAAATATTTTC-T
**
165699 ATTATATTTTTTAATATTTTCT
1 ATTA-ATTTTAAAATATTTTCT
165721 ATTAATTTT
1 ATTAATTTT
165730 TTCATATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.19
22 5 0.19
23 16 0.59
24 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTAATTTTAAAATATTTTCT
Found at i:168030 original size:65 final size:64
Alignment explanation
Indices: 167829--168038 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
167819 TGGACCCTTA
* ** ** *
167829 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATTCTCAGTGCATCGATGCATGGTTG
* *
167893 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATTCTCAGTGCATCGGTGCATAGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATTCTCAGTGCATCGATGCATGGT-T
167958 -
64 G
* ** *
167958 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCAT-GGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATTC-TCAGTGCATCGATGCATGG-T
168021 TG
63 TG
* *
168023 GTACATCGGTGCATCA
1 GTGCATCGATGCATCA
168039 CTCTAAAAAA
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
63 3 0.02
64 50 0.41
65 65 0.53
66 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATTCTCAGTGCATCGATGCATGGTTG
Found at i:168731 original size:31 final size:31
Alignment explanation
Indices: 168692--168762 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
168682 AGAGTCGAGG
*
168692 GTTTACCTAT-GTCTTTCGAGACATATGGACA
1 GTTTACCTATAGTCTAT-GAGACATATGGACA
* * *
168723 TTTTACCTATATTCTATGAGACATATGGATA
1 GTTTACCTATAGTCTATGAGACATATGGACA
168754 GTTTACCTA
1 GTTTACCTA
168763 GGTTCTTCAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (31 bp):
GTTTACCTATAGTCTATGAGACATATGGACA
Found at i:171205 original size:37 final size:37
Alignment explanation
Indices: 171155--171231 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
171145 ACAAAAATAA
171155 AATTTTAAGATAGTTACCTTTAATAAAATGAACGACT
1 AATTTTAAGATAGTTACCTTTAATAAAATGAACGACT
*
171192 AATTTTAAGATAGTTACCTTTAGTAAAATGAACGACT
1 AATTTTAAGATAGTTACCTTTAATAAAATGAACGACT
171229 AAT
1 AAT
171232 ATAAAAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (37 bp):
AATTTTAAGATAGTTACCTTTAATAAAATGAACGACT
Found at i:171996 original size:130 final size:130
Alignment explanation
Indices: 171793--172040 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
171783 AATTTTCTTC
* * * *
171793 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATATGCTAACACATGTCAGAT
*
171858 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * ** *
171923 TAATTAGGTGGTAACACGTGTCACCAATGACATGTGTCATGATCATATGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATATGCTAACACATGTCAGAT
171988 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
172041 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATATGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:179265 original size:31 final size:32
Alignment explanation
Indices: 179230--179306 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
179220 TTAACTCGGG
** *
179230 GTGACTACATCTTAATTACGTAAAAA-TAAAA
1 GTGACTACATCTTAATTAAATAAAAACAAAAA
* *
179261 GTGACCACATTTTAATTAAATAAAAACAAAAA
1 GTGACTACATCTTAATTAAATAAAAACAAAAA
*
179293 GTGACTATATCTTA
1 GTGACTACATCTTA
179307 TATTTTTCGA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 22 0.59
32 15 0.41
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (32 bp):
GTGACTACATCTTAATTAAATAAAAACAAAAA
Found at i:180732 original size:20 final size:20
Alignment explanation
Indices: 180707--180757 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
180697 TTTTCCCAAT
*
180707 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
180727 TCGCAATGCGAATTTGAAAA
1 TCGCAATGCGAATAAGAAAA
180747 TCGCAATGCGA
1 TCGCAATGCGA
180758 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:180769 original size:20 final size:20
Alignment explanation
Indices: 180747--180875 Score: 170
Period size: 20 Copynumber: 6.4 Consensus size: 20
180737 AATTTGAAAA
* *
180747 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
* **
180767 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
180788 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
180808 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
180828 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
180848 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
180868 TCGCAACG
1 TCGCAACG
180876 AGATTCTGAA
Statistics
Matches: 99, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
19 2 0.02
20 80 0.81
21 15 0.15
22 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:180789 original size:61 final size:61
Alignment explanation
Indices: 180724--180839 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
180714 GCGAATAAGT
* * *
180724 AAATCGCAATGCGA-ATTTGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATA-CTGAAAATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
*** *
180785 AAATCGCAACGCGATACTGACTTTCGCAACGCGATACTGACTTTCGCAACGCGAT
1 AAATCGCAACGCGATACTGAAAATCGCAACGCGATACTGACTATCGCAACGCGAT
180840 TCTGACTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 46 0.98
62 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (61 bp):
AAATCGCAACGCGATACTGAAAATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
Found at i:180799 original size:41 final size:42
Alignment explanation
Indices: 180743--180859 Score: 159
Period size: 41 Copynumber: 2.9 Consensus size: 42
180733 TGCGAATTTG
* *
180743 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT-AC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
*
180784 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
** *
180826 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGAT
180860 TCTGACTTTC
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
40 31 0.45
41 36 0.52
42 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
Found at i:180874 original size:60 final size:60
Alignment explanation
Indices: 180747--180893 Score: 170
Period size: 60 Copynumber: 2.4 Consensus size: 60
180737 AATTTGAAAA
*
180747 TCGCAATGCGATACTGACTATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTATCGCAACGCGATAATAC-AAATCGCAACGCGATACTGACTT
* ** ** *
180808 TCGCAACGCGATACTGACTTTCGCAACGCGATTCTGAC-TTTCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTATCGCAACGCGATAAT-ACAAATCGCAACGCGATACTGACTT
* * **
180868 TCGCAACGAGATTCTGAAAATCGCAA
1 TCGCAACGCGATACTGACTATCGCAA
180894 TCATCTTCAA
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
60 40 0.55
61 31 0.42
62 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (60 bp):
TCGCAACGCGATACTGACTATCGCAACGCGATAATACAAATCGCAACGCGATACTGACTT
Found at i:180892 original size:40 final size:40
Alignment explanation
Indices: 180808--180893 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
180798 ATACTGACTT
* ***
180808 TCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTTTCGCAACGAGATTCTGAAAA
*
180848 TCGCAACGCGATTCTGACTTTCGCAACGAGATTCTGAAAA
1 TCGCAACGCGATACTGACTTTCGCAACGAGATTCTGAAAA
180888 TCGCAA
1 TCGCAA
180894 TCATCTTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
TCGCAACGCGATACTGACTTTCGCAACGAGATTCTGAAAA
Found at i:181152 original size:19 final size:20
Alignment explanation
Indices: 181096--181170 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
181086 CAACGGGGAA
*
181096 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
181116 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
181136 ATCGCAACGCG-AAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
181155 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
181171 CGCAATGCGA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.35
20 34 0.65
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:181226 original size:52 final size:53
Alignment explanation
Indices: 181170--181277 Score: 119
Period size: 52 Copynumber: 2.1 Consensus size: 53
181160 AACGAGAAAA
* *
181170 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTATCGTTGCGATAGCCA-TT
1 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTATCATTGCGATAGCCAGTT
* ** * ** * *
181222 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCATTGCGATAGTCAGTT
1 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTATCATTGCGATAGCCAGTT
181275 TCG
1 TCG
181278 TGTTGCGATT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
52 40 0.89
53 5 0.11
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (53 bp):
TCGCAATGCGAAATGAAAATCGCATTGCGATTCTATCATTGCGATAGCCAGTT
Found at i:181232 original size:19 final size:19
Alignment explanation
Indices: 181208--181252 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
181198 GATTTTATCG
*
181208 TTGCGATAGCCATTTCGCA
1 TTGCGATAGCAATTTCGCA
***
181227 TTGCGATTTTAATTTCGCA
1 TTGCGATAGCAATTTCGCA
181246 TTGCGAT
1 TTGCGAT
181253 TCTCTCATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (19 bp):
TTGCGATAGCAATTTCGCA
Found at i:181262 original size:33 final size:33
Alignment explanation
Indices: 181225--181352 Score: 139
Period size: 33 Copynumber: 3.8 Consensus size: 33
181215 AGCCATTTCG
* *
181225 CATTGCGATTTTAATTTCGCATTGCGATTCTCT
1 CATTGCGATTTTAATTTCGCATTGCGATTTTGT
* * * **
181258 CATTGCGATAGTCAGTTTCGTGTTGCGATTTTGT
1 CATTGCGAT-TTTAATTTCGCATTGCGATTTTGT
* *
181292 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
1 CATTGCGATTTTAATTTCGCATTGCGATTTTGT
* * *
181325 CGTTGAGATTTTCATTTCGCATTGCGAT
1 CATTGCGATTTTAATTTCGCATTGCGAT
181353 AGCCATTTCC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
33 54 0.68
34 25 0.32
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (33 bp):
CATTGCGATTTTAATTTCGCATTGCGATTTTGT
Found at i:181298 original size:14 final size:14
Alignment explanation
Indices: 181279--181336 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
181269 TCAGTTTCGT
181279 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
*
181293 GTTGCGATTTTCATTTC
1 GTTGCGA-TTT--TGTC
181310 GCATTGCGATTTTGTC
1 G--TTGCGATTTTGTC
*
181326 GTTGAGATTTT
1 GTTGCGATTTT
181337 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.17
ACGTcount: A:0.12, C:0.14, G:0.24, T:0.50
Consensus pattern (14 bp):
GTTGCGATTTTGTC
Found at i:181391 original size:20 final size:20
Alignment explanation
Indices: 181337--181380 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
181327 TTGAGATTTT
181337 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
181356 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
181376 CATTT
1 CATTT
181381 TCGTGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:181949 original size:18 final size:18
Alignment explanation
Indices: 181926--181973 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
181916 CGGGTCGATC
181926 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
181944 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
181962 AGGTGATGGCTC
1 AGGTGATGGCTC
181974 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:183337 original size:20 final size:20
Alignment explanation
Indices: 183289--183347 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
183279 AATAGTTTCT
* *
183289 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
183309 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
183329 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
183348 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:183876 original size:40 final size:41
Alignment explanation
Indices: 183826--183939 Score: 149
Period size: 40 Copynumber: 2.8 Consensus size: 41
183816 GATTATGTAT
* *
183826 TATCTCGTTGCGAAAGTCAGTATTGCGTTGCGAAATT-AAG
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAATTGAAG
** * *
183866 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAATTGAAG
* *
183907 TATCGCGTTGCGATAGTCAGTATCACGTTGCGA
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGA
183940 TTTTTCAAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 33 0.51
41 32 0.49
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAATTGAAG
Found at i:183925 original size:41 final size:41
Alignment explanation
Indices: 183806--183943 Score: 179
Period size: 41 Copynumber: 3.4 Consensus size: 41
183796 CGTTTTGAAA
* * *
183806 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** * *
183847 ATTGCGTTGCGAAATT-AAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
183887 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
183928 ATCACGTTGCGATTTT
1 ATCGCGTTGCGATTTT
183944 TCAAATTCGC
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 34 0.42
41 47 0.58
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:183940 original size:20 final size:20
Alignment explanation
Indices: 183826--183939 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
183816 GATTATGTAT
*
183826 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
183846 TATTGCGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
183866 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
183886 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
183907 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
183927 TATCACGTTGCGA
1 TATCGCGTTGCGA
183940 TTTTTCAAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 59 0.76
21 14 0.18
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:183959 original size:41 final size:41
Alignment explanation
Indices: 183833--183998 Score: 135
Period size: 41 Copynumber: 4.0 Consensus size: 41
183823 TATTATCTCG
* * ** * *
183833 TTGCGAAAGTCAGTATTGCGTTGCGA-AATT-AAGTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTTCAAAT-TCGCA
* * *
183873 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGT--ATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTT-TCAAAT-TCGCA
*
183914 TTGCGATAGTCAGTATCACGTTGCGATTTTTCAAATTCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTTCAAATTCGCA
** *
183955 TTGCGATTTTCCA-AATTCGCGTTGCGATTTTTCAAATTCGCA
1 TTGCGATAGT-CAGTA-TCGCGTTGCGATTTTTCAAATTCGCA
183997 TT
1 TT
183999 ACGAATCTGG
Statistics
Matches: 108, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
40 26 0.24
41 50 0.46
42 32 0.30
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTTCAAATTCGCA
Found at i:183960 original size:21 final size:21
Alignment explanation
Indices: 183934--183998 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
183924 CAGTATCACG
183934 TTGCGATTTTTCAAATTCGCA
1 TTGCGATTTTTCAAATTCGCA
* *
183955 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTTCAAATTCGCA
183976 TTGCGATTTTTCAAATTCGCA
1 TTGCGATTTTTCAAATTCGCA
183997 TT
1 TT
183999 ACGAATCTGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (21 bp):
TTGCGATTTTTCAAATTCGCA
Found at i:192221 original size:31 final size:31
Alignment explanation
Indices: 192181--192249 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
192171 ATATAAGATA
* **
192181 TAGTCACTTTTGTTTTTATTTAATTAAAATG
1 TAGTCACTTTTATTTTTACGTAATTAAAATG
* *
192212 TGGTCACTTTTATTTTTACGTAATTAAGATG
1 TAGTCACTTTTATTTTTACGTAATTAAAATG
192243 TAGTCAC
1 TAGTCAC
192250 CCCGAGTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (31 bp):
TAGTCACTTTTATTTTTACGTAATTAAAATG
Found at i:197289 original size:19 final size:18
Alignment explanation
Indices: 197267--197364 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 18
197257 AAAAATTACT
197267 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
197286 ATCGCAA-CGAGATG---
1 ATCGCAAGCGAAATGAAA
197300 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
197319 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
197333 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
197352 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
197365 TTTAGTTTCG
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
14 14 0.23
15 3 0.05
16 8 0.13
17 8 0.13
18 3 0.05
19 26 0.42
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:197309 original size:33 final size:33
Alignment explanation
Indices: 197267--197360 Score: 154
Period size: 33 Copynumber: 2.8 Consensus size: 33
197257 AAAAATTACT
*
197267 ATCGCAATGCGAAATGAAAATCGCAACGAGATG-
1 ATCGCAATGCGAAATGAAAATCGCAACGAG-GGA
197300 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
*
197333 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
197361 CGAATTTAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 1 0.02
33 57 0.98
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
Found at i:197395 original size:19 final size:19
Alignment explanation
Indices: 197360--197405 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
197350 AAATCGCAAC
*
197360 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
197379 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
197398 ACGATTTT
1 GCGATTTT
197406 GTCGTTGCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:197561 original size:14 final size:14
Alignment explanation
Indices: 197542--197578 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
197532 CATCAATTAA
197542 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
197556 ACAAATCACCTTTT
1 ACAAATCAACTTTT
197570 ACAAATCAA
1 ACAAATCAA
197579 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:199014 original size:42 final size:42
Alignment explanation
Indices: 198968--199047 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
198958 CGATGACAGT
* * *
198968 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
199010 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
199048 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:199444 original size:91 final size:90
Alignment explanation
Indices: 199269--199453 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
199259 ATTTCAAACT
* * *
199269 TTCAACTAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
199334 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
199362 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
199426 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
199453 T
1 T
199454 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 42 0.49
93 17 0.20
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:201170 original size:20 final size:20
Alignment explanation
Indices: 201145--201182 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
201135 TCTTTTGGTT
201145 GAAATGAAAATCGCAACGCG
1 GAAATGAAAATCGCAACGCG
**
201165 GAAATGACTATCGCAACG
1 GAAATGAAAATCGCAACG
201183 AGAGAATCGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (20 bp):
GAAATGAAAATCGCAACGCG
Found at i:201193 original size:14 final size:14
Alignment explanation
Indices: 201174--201234 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
201164 GGAAATGACT
*
201174 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
201188 ATCGCAACACGAAATGAAA
1 ATCGC-A-ACG--A-GAAA
*
201207 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
*
201221 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
201235 TGAAAATCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 20 0.53
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 8 0.21
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:201211 original size:33 final size:33
Alignment explanation
Indices: 201153--201242 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
201143 TTGAAATGAA
**
201153 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
* *
201187 AATCGCAACACGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
201220 AATCGCAACGCGAAATGAAAATC
1 AATCGCAACGCGAAATGAAAATC
201243 ACAATGCGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 41 0.80
34 10 0.20
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:201295 original size:33 final size:32
Alignment explanation
Indices: 201247--201339 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 32
201237 AAAATCACAA
*
201247 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTT-ATTTCGCGTTGCGATTATCTCGT
*
201280 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTT-ATTTCGCGTTGCGATTATCTCGT
*
201313 TGCGATAGTTATTTCCGCGTTGCGATT
1 TGCGAT-TTTATTT-CGCGTTGCGATT
201340 TTCATTCTCG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
33 40 0.74
34 14 0.26
ACGTcount: A:0.11, C:0.20, G:0.25, T:0.44
Consensus pattern (32 bp):
TGCGATTTTATTTCGCGTTGCGATTATCTCGT
Found at i:201301 original size:19 final size:19
Alignment explanation
Indices: 201277--201345 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 19
201267 GCGATTATCT
201277 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
201296 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
201310 CGTTGCGATAGTT-ATTTCCG
1 CGTTGCGAT-TTTCATTT-CG
201330 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
201346 CTCGAAACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 15
0.68 0.05 0.26
Matches are distributed among these distances:
14 10 0.26
17 5 0.13
19 11 0.28
20 13 0.33
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:201889 original size:20 final size:20
Alignment explanation
Indices: 201864--201975 Score: 64
Period size: 20 Copynumber: 5.5 Consensus size: 20
201854 GCTATGTAAA
201864 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* * *
201884 TCGCATTTCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
201904 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* * ** *
201925 TCGCATTGCTATTTACTTAA
1 TCGCATTGCGATGTAAGTAT
* * *
201945 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
201965 TCGCATTGCGA
1 TCGCATTGCGA
201976 ATTATGAAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
19 3 0.04
20 55 0.73
21 17 0.23
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:201939 original size:41 final size:40
Alignment explanation
Indices: 201882--201975 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 40
201872 CGATAGTAAG
* * *
201882 ATTCGCATTTCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * * *
201922 AATTCGCATTGCTATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
201963 ATTCGCATTGCGA
1 ATTCGCATTGCGA
201976 ATTATGAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 12 0.27
41 33 0.73
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.41
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:201988 original size:41 final size:42
Alignment explanation
Indices: 201943--202121 Score: 113
Period size: 41 Copynumber: 4.4 Consensus size: 42
201933 CTATTTACTT
* * * * *
201943 AATCGCGTTGCGATTTACGT-ATTCGCATTGCGAATTATGAA
1 AATCGCATTGCGATATACGTAAATCGCAATGCGAATTAGGAA
**
201984 AATCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAA
1 AATCGCATTGCGATATACGTAAATCGCAATGCGAATTAGGAA
* * * ***
202025 AATTGCATTGCGATAGT-CAGT--ATCGCATTGCGATTTA-CTT
1 AATCGCATTGCGATA-TAC-GTAAATCGCAATGCGAATTAGGAA
* * * *
202065 ATTCGCATTGCGA-ATTAGGAAAATCGCAACGCGAAATT-GGAA
1 AATCGCATTGCGATA-TACGTAAATCGCAATGCG-AATTAGGAA
202107 AATCGCATTGCGATA
1 AATCGCATTGCGATA
202122 GTCATAATCG
Statistics
Matches: 101, Mismatches: 27, Indels: 18
0.69 0.18 0.12
Matches are distributed among these distances:
39 3 0.03
40 16 0.16
41 61 0.60
42 17 0.17
43 4 0.04
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (42 bp):
AATCGCATTGCGATATACGTAAATCGCAATGCGAATTAGGAA
Found at i:201996 original size:21 final size:21
Alignment explanation
Indices: 201972--202027 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
201962 TATTCGCATT
*
201972 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
201993 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
202013 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
202028 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:202036 original size:21 final size:21
Alignment explanation
Indices: 201965--202119 Score: 77
Period size: 21 Copynumber: 7.5 Consensus size: 21
201955 ATTTACGTAT
* *
201965 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
201986 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
202006 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* * * **
202027 TTGCATTGCGATAGT-C-AGTA
1 TCGCAATGCGA-ATTACGAAAA
* * ** *
202047 TCGCATTGCGATTTAC-TTAT
1 TCGCAATGCGAATTACGAAAA
* *
202067 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
202088 TCGCAACGCGAAATT-GGAAAA
1 TCGCAATGCG-AATTACGAAAA
*
202109 TCGCATTGCGA
1 TCGCAATGCGA
202120 TAGTCATAAT
Statistics
Matches: 100, Mismatches: 29, Indels: 11
0.71 0.21 0.08
Matches are distributed among these distances:
19 1 0.01
20 45 0.45
21 48 0.48
22 6 0.06
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:202051 original size:82 final size:82
Alignment explanation
Indices: 201965--202141 Score: 200
Period size: 82 Copynumber: 2.2 Consensus size: 82
201955 ATTTACGTAT
* *
201965 TCGCATTGCGAATTA-TGAAAATCGCAACGCGAA-TACGTAAATCGCAATGCG-AATTAGGAAAA
1 TCGCATTGCGAATTACT--AAATCGCAACGCGAATTACGAAAATCGCAACGCGAAATT-GGAAAA
*
202027 TTGCATTGCGATAGTCAGT-A
63 TCGCATTGCGATAGTCA-TAA
* * * ** *
202047 TCGCATTGCGATTTACTTATTCGCATTGCGAATTAGGAAAATCGCAACGCGAAATTGGAAAATCG
1 TCGCATTGCGAATTACTAAATCGCAACGCGAATTACGAAAATCGCAACGCGAAATTGGAAAATCG
202112 CATTGCGATAGTCATAA
66 CATTGCGATAGTCATAA
*
202129 TCGCGTTGCGAAT
1 TCGCATTGCGAAT
202142 CTGGAAACTG
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
81 12 0.15
82 63 0.79
83 5 0.06
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (82 bp):
TCGCATTGCGAATTACTAAATCGCAACGCGAATTACGAAAATCGCAACGCGAAATTGGAAAATCG
CATTGCGATAGTCATAA
Found at i:205836 original size:29 final size:29
Alignment explanation
Indices: 205792--205865 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
205782 TCGTTGATCA
*
205792 GGTGCTATTTTAGTAATTATTTCTAAAAG
1 GGTGCTATTTTCGTAATTATTTCTAAAAG
* *
205821 GGTGCTATTTTCGTAATTATTTTTAAGAG
1 GGTGCTATTTTCGTAATTATTTCTAAAAG
205850 GGTGCTATTTTCGTAA
1 GGTGCTATTTTCGTAA
205866 AATGGTTGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (29 bp):
GGTGCTATTTTCGTAATTATTTCTAAAAG
Found at i:206601 original size:24 final size:24
Alignment explanation
Indices: 206566--206638 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
206556 ATTTTTGACG
206566 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACTTGACCT
* * *
206590 GGATTTTTATATGATACATGACAT
1 GGATTTTGATATGATACTTGACCT
* * *
206614 GGATTCTGATCTGCTACTTGACCT
1 GGATTTTGATATGATACTTGACCT
206638 G
1 G
206639 AATTATGCTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (24 bp):
GGATTTTGATATGATACTTGACCT
Found at i:206662 original size:2 final size:2
Alignment explanation
Indices: 206655--206691 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
206645 GCTTTAAATT
206655 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
206692 CCGTTATGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.